SAN FRANCISCO — DNA sequencing giant Illumina on Monday introduced a powerful new line of its instruments, bringing down the average time of sequencing a human genome to one hour — from more than one day just a couple of years ago.

The San Diego company’s announcement is the latest step toward the dream of making genomic analysis a near-universal part of medicine, enabling easier and less costly detection of rare diseases and the ability to link genetic variations with health and illness. As sequencing prices fall and capacity rises, uses of the technology that were once impractical become feasible.

And “one day,” Illumina chief executive Francis DeSouza said, the company’s NovaSeq line is expected to reduce the cost of sequencing to $100 per human genome. That would be one-tenth the figure that Illumina announced in 2014, when it achieved the milestone of $1,000 per genome. A decade ago, the expense was about $10 million.

The $100 mark could be reached a few years from now, DeSouza implied in his talk at the JP Morgan Healthcare Conference in San Francisco. That was the same conference Illumina used to introduce its $1,000-busting version of its HiSeq line. The NovaSeq line needs to be optimized, just as with the HiSeq one, he said.

Illumina said shipping of the NovaSeq 6000 is scheduled to start in March and that NovaSeq 5000 will begin shipping midyear. The NovaSeq 5000 and 6000 systems are priced at $850,000 and $985,000, respectively.

These machines can also be purchased individually, unlike the HiSeq line, and that could expand the number of medical and research institutions that could afford them. The lowest price for HiSeq — Illumina’s former top-end system — is a base $6 million for a set of five machines. Originally, the system sold in sets of 10 for $10 million a system.

courtesy photo

Illumina is headquartered in San Diego.

Illumina is headquartered in San Diego. (courtesy photo)

Biotech researchers regard Illumina as the dominant maker of DNA sequencers. With a market value of more than $20 billion, Illumina is also the biggest publicly traded biotech company in San Diego County. Its value is based on both its continued technological progress and the demand for these advancements in the biotech sector.

Investors appeared to like the announcement, which was made after the close of regular trading Monday. Illumina’s shares rose in after-hours trading to $165.01 each, up $23.47 or 16.6 percent.

More uses

The greatly increased sequencing speed will enable more applications and a larger scale for genomic sequencing for medicine, said genomics pioneer J. Craig Venter, whose Human Longevity company in La Jolla has already ordered the new system. Venter, who helped lead sequencing of the first human genome, has been an Illumina customer for years.

“Faster, inexpensive and innovative sequencing technology is a key component driving breakthroughs in precision medicine,” said Venter, referring to the growing push by scientific, medical and government leaders to customize medical care for each person. “This technology is also enabling (Human Longevity) to expand (its) database, the world’s most comprehensive database of genomic, phenotypic and clinical data.”

More precise and thorough DNA sequencing is a major part of the precision-medicine field, with the goal of taking every medically significant fact learned about a patient and using that knowledge to select the best treatment for him or her — and to develop new treatments based on the resulting knowledge.

Two years ago, President Barack Obama introduced the federal Precision Medicine Initiative to lead and coordinate efforts in the government and private sector.

In addition, Illumina’s high-volume, industrial-capacity sequencing machines are key to ever-growing research efforts to look for genetic patterns — and variants — among millions of people that could unlock mysteries about the causes of various diseases.

In San Diego, a $207 million effort to deeply explore the health of 1 million patients is being led by Dr. Eric Topol, a Scripps Health cardiologist and geneticist. The grant from the National Institutes of Health is part of the federal initiative that Obama rolled out. Studies like this one reflect the other side of DNA sequencing — making sense of what all the huge amounts of generated data actually mean. Such analysis imposes its own costs, which aren’t included in the raw price tag of a sequenced genome.

Topol said the reduction in cost will allow many more labs and companies to enter the high-level DNA sequencing market, although he believed the expense is still high.

“The $100 genome that the Illumina CEO projected is speculation,” Topol said. “Someday we’ll get there, for sure. But when, and with which platform, remains to be seen.”

Entire genome

A human genome contains about 3 billion letters of the genetic alphabet — the string of A, C, G, and T that represent genes and other elements of DNA.

Processing this information takes immense computing power. And because actual genes represent only a small percentage of the DNA in a genome, many diagnostic tests keep costs down by focusing only on that part, which is called the exome.

However, scientists have discovered medical significance in numerous stretches of DNA outside of genes. These important areas are missed in exome sequencing.

DeSouza said the increased capacity brought about by NovaSeq should help make full-genome sequencing more affordable — and thus more routine.

One use of this increased capacity is to conduct repeated genomic sequencing of cancer patients, whose tumors frequently mutate. Being able to keep up with the mutations will allow doctors to better guide therapy, such as by discovering when cancer cells have become resistant to certain drugs.

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